Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
Swanson, Elliott, Lord, Cara, Reading, Julian, Heubeck, Alexander T, Genge, Palak C, Thomson, Zachary, Weiss, Morgan DA, Li, Xiao-Jun, Savage, Adam K, Green, Richard R, Torgerson, Troy R, Bumol, Thomas F, Graybuck, Lucas T, Skene, Peter J
Published in eLife (09.04.2021)
Published in eLife (09.04.2021)
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Neuronal MeCP2 Is Expressed at Near Histone-Octamer Levels and Globally Alters the Chromatin State
Skene, Peter J., Illingworth, Robert S., Webb, Shaun, Kerr, Alastair R.W., James, Keith D., Turner, Daniel J., Andrews, Rob, Bird, Adrian P.
Published in Molecular cell (26.02.2010)
Published in Molecular cell (26.02.2010)
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BarWare: efficient software tools for barcoded single-cell genomics
Swanson, Elliott, Reading, Julian, Graybuck, Lucas T, Skene, Peter J
Published in BMC bioinformatics (27.03.2022)
Published in BMC bioinformatics (27.03.2022)
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Journal Article
Persistent serum protein signatures define an inflammatory subcategory of long COVID
Talla, Aarthi, Vasaikar, Suhas V., Szeto, Gregory Lee, Lemos, Maria P., Czartoski, Julie L., MacMillan, Hugh, Moodie, Zoe, Cohen, Kristen W., Fleming, Lamar B., Thomson, Zachary, Okada, Lauren, Becker, Lynne A., Coffey, Ernest M., De Rosa, Stephen C., Newell, Evan W., Skene, Peter J., Li, Xiaojun, Bumol, Thomas F., Juliana McElrath, M., Torgerson, Troy R.
Published in Nature communications (09.06.2023)
Published in Nature communications (09.06.2023)
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CpG islands influence chromatin structure via the CpG-binding protein Cfp1
Illingworth, Robert, Thomson, John P, Deaton, Aimée, James, Keith D, Skene, Peter J, Bird, Adrian, Clouaire, Thomas, Webb, Shaun, Kerr, Alastair R. W, Selfridge, Jim, Turner, Daniel J, Guy, Jacky, Andrews, Rob
Published in Nature (15.04.2010)
Published in Nature (15.04.2010)
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The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1
Skene, Peter J, Hernandez, Aaron E, Groudine, Mark, Henikoff, Steven
Published in eLife (15.04.2014)
Published in eLife (15.04.2014)
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MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts
Rachid Zaim, Samir, Pebworth, Mark-Phillip, McGrath, Imran, Okada, Lauren, Weiss, Morgan, Reading, Julian, Czartoski, Julie L., Torgerson, Troy R., McElrath, M. Juliana, Bumol, Thomas F., Skene, Peter J., Li, Xiao-jun
Published in Nature communications (09.08.2024)
Published in Nature communications (09.08.2024)
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A comprehensive platform for analyzing longitudinal multi-omics data
Vasaikar, Suhas V., Savage, Adam K., Gong, Qiuyu, Swanson, Elliott, Talla, Aarthi, Lord, Cara, Heubeck, Alexander T., Reading, Julian, Graybuck, Lucas T., Meijer, Paul, Torgerson, Troy R., Skene, Peter J., Bumol, Thomas F., Li, Xiao-jun
Published in Nature communications (27.03.2023)
Published in Nature communications (27.03.2023)
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Journal Article
DUX4-Induced Histone Variants H3.X and H3.Y Mark DUX4 Target Genes for Expression
Resnick, Rebecca, Wong, Chao-Jen, Hamm, Danielle C., Bennett, Sean R., Skene, Peter J., Hake, Sandra B., Henikoff, Steven, van der Maarel, Silvère M., Tapscott, Stephen J.
Published in Cell reports (Cambridge) (12.11.2019)
Published in Cell reports (Cambridge) (12.11.2019)
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Journal Article
Transcriptional regulatory networks underlying gene expression changes in Huntington's disease
Ament, Seth A, Pearl, Jocelynn R, Cantle, Jeffrey P, Bragg, Robert M, Skene, Peter J, Coffey, Sydney R, Bergey, Dani E, Wheeler, Vanessa C, MacDonald, Marcy E, Baliga, Nitin S, Rosinski, Jim, Hood, Leroy E, Carroll, Jeffrey B, Price, Nathan D
Published in Molecular systems biology (01.03.2018)
Published in Molecular systems biology (01.03.2018)
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Multimodal analysis for human ex vivo studies shows extensive molecular changes from delays in blood processing
Savage, Adam K., Gutschow, Miriam V., Chiang, Tony, Henderson, Kathy, Green, Richard, Chaudhari, Monica, Swanson, Elliott, Heubeck, Alexander T., Kondza, Nina, Burley, Kelli C., Genge, Palak C., Lord, Cara, Smith, Tanja, Thomson, Zachary, Beaubien, Aldan, Johnson, Ed, Goldy, Jeff, Bolouri, Hamid, Buckner, Jane H., Meijer, Paul, Coffey, Ernest M., Skene, Peter J., Torgerson, Troy R., Li, Xiao-jun, Bumol, Thomas F.
Published in iScience (21.05.2021)
Published in iScience (21.05.2021)
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Optimized workflow for human PBMC multiomic immunosurveillance studies
Genge, Palak C., Roll, Charles R., Heubeck, Alexander T., Swanson, Elliott, Kondza, Nina, Lord, Cara, Weiss, Morgan, Hernandez, Veronica, Phalen, Cole, Thomson, Zachary, Torgerson, Troy R., Skene, Peter J., Bumol, Thomas F., Reading, Julian
Published in STAR protocols (17.12.2021)
Published in STAR protocols (17.12.2021)
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Mechanism of Initiation Site Selection Promoted by the Human Rhinovirus 2 Internal Ribosome Entry Site
Kaminski, Ann, Pöyry, Tuija A. A., Skene, Peter J., Jackson, Richard J.
Published in Journal of Virology (01.07.2010)
Published in Journal of Virology (01.07.2010)
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Journal Article
Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment
Thomson, Zachary, He, Ziyuan, Swanson, Elliott, Henderson, Katherine, Phalen, Cole, Zaim, Samir Rachid, Pebworth, Mark-Phillip, Okada, Lauren Y., Heubeck, Alexander T., Roll, Charles R., Hernandez, Veronica, Weiss, Morgan, Genge, Palak C., Reading, Julian, Giles, Josephine R., Manne, Sasikanth, Dougherty, Jeanette, Jasen, C. J., Greenplate, Allison R., Becker, Lynne A., Graybuck, Lucas T., Vasaikar, Suhas V., Szeto, Gregory L., Savage, Adam K., Speake, Cate, Buckner, Jane H., Li, Xiao-jun, Bumol, Thomas F., Wherry, E.John, Torgerson, Troy R., Vella, Laura A., Henrickson, Sarah E., Skene, Peter J., Gustafson, Claire E.
Published in Nature immunology (01.11.2023)
Published in Nature immunology (01.11.2023)
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Journal Article
Author Correction: Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment
Thomson, Zachary, He, Ziyuan, Swanson, Elliott, Henderson, Katherine, Phalen, Cole, Zaim, Samir Rachid, Pebworth, Mark-Phillip, Okada, Lauren Y., Heubeck, Alexander T., Roll, Charles R., Hernandez, Veronica, Weiss, Morgan, Genge, Palak C., Reading, Julian, Giles, Josephine R., Manne, Sasikanth, Dougherty, Jeanette, Jasen, C. J., Greenplate, Allison R., Becker, Lynne A., Graybuck, Lucas T., Vasaikar, Suhas V., Szeto, Gregory L., Savage, Adam K., Speake, Cate, Buckner, Jane H., Li, Xiao-jun, Bumol, Thomas F., Wherry, E.John, Torgerson, Troy R., Vella, Laura A., Henrickson, Sarah E., Skene, Peter J., Gustafson, Claire E.
Published in Nature immunology (01.03.2024)
Published in Nature immunology (01.03.2024)
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